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babaksaremi / RESEQ

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FASTQ from 16S #1

Open emamm1 opened 2 years ago

emamm1 commented 2 years ago

Hello,

Thanks for this nice tool

I am trying to apply the method on 16S fastq. The taxonomy sequence for bacteria could be downloaded from NCBI however I don't understand

1- which .dmp file I should use in the taxdump 2- If I want to filter the file in 1- to include only bacteria as you did with virus what tool should I use

Best,

babaksaremi commented 2 years ago

Hi emamm1,

sry for the late answear. If you download the newest taxonomy dump there should be a file contained named "fullnamelineage.dmp". From there i didn't use a specific tool. If you are working in a linux environment you just could type: cat fullnamelineage.dmp | grep Bacteria > YOURNEWFILE.dmp This should give you your taxonomy file for all bacterias. Hope this helps

Best